S1 Fig. Experimental set-up and differentially expressed genes (DEGs)
S1 Fig. Experimental set-up and differentially expressed genes (DEGs)
A) RNA sampling conditions from environmental (soil and mineral water) and previously obtained samples (rich B medium reference and three in planta conditions). B) Transcriptomic data analysis pipeline. First, raw RNA-seq data quality was evaluated with FastQC (v.0.11.5), trimmed with trimGalore (v.0.6.1) and potential rRNA contaminants were filtered out with the SortMeRNA software (v.4.2.0). Reads were mapped with Bowtie2 (v. 2.4.4) and alignments quantified with FADU v. 1.8. The R. solanacearum UY031 genome GCF_001299555.1_ASM129955v1 was used. DEG analyses were performed with Deseq2 (v. 1.34.0). Genes with |log2(fold-change)|>1.5 and adjusted p-value <0.01 were considered as differentially expressed (DEG) when compared to the reference medium. The UpsetR package (v. 1.4.0) (90) was used to detect unique DEG and intersections among the in the different conditions. Deseq2 transformed counts normalized for sample size were used for principal component analysis. C) DEGs in the different conditions. Bars show the total number of up- (yellow) and downregulated (blue) genes for each condition compared to the reference Rich B medium. The line graph and the right Y axis indicate the percentage of DEGs. Drawings created with BioRender.
Peer reviewed
Ralstonia solanacearum </, Phenylacetate catabolism, Alkaline ph, Life cycle, Function experiments, Potential disease outbreaks, Culturability associated, Providing valuable insights, Bacterial pathogens exhibit, Premature induction, div >< p, Bacterial wilt disease, Downregulated virulence, Solanacearum </, Bacterial survival, Control dissemination, Intriguing induction, Diverse ecological niches, Non culturable state, Planta </, Remarkable ability, Environments occupied, Late xylem colonization, Oxidative stress response, Alternate carbon sources, t3ss )., Upregulated stress, Life cycle allow, Bacterial reservoirs, r </, Causing agent, Mechanisms enabling, Catalase katg, Regulator oxyr, Bacterial plant pathogen, Glyoxylate cycle, Gene expression, vbnc )., Two environments, t3ss induction, Investigate pathogen adaptation, Deletion cause
Ralstonia solanacearum </, Phenylacetate catabolism, Alkaline ph, Life cycle, Function experiments, Potential disease outbreaks, Culturability associated, Providing valuable insights, Bacterial pathogens exhibit, Premature induction, div >< p, Bacterial wilt disease, Downregulated virulence, Solanacearum </, Bacterial survival, Control dissemination, Intriguing induction, Diverse ecological niches, Non culturable state, Planta </, Remarkable ability, Environments occupied, Late xylem colonization, Oxidative stress response, Alternate carbon sources, t3ss )., Upregulated stress, Life cycle allow, Bacterial reservoirs, r </, Causing agent, Mechanisms enabling, Catalase katg, Regulator oxyr, Bacterial plant pathogen, Glyoxylate cycle, Gene expression, vbnc )., Two environments, t3ss induction, Investigate pathogen adaptation, Deletion cause
selected citations These citations are derived from selected sources.This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).0 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Average influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Average impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Average
Citations provided by BIP!Popularity provided by BIP!